From: Ben Houston (ben@exocortex.org)
Date: Tue Feb 13 2001 - 01:52:24 MST
It's not just the shape that is important but the amino acids that make up
the shape. It's the specific amino acid sequences and their shape that give
it the function not just the shape. The specific amino acids determine the
hydrophobic/hydrophilic-ness of a region as well as the potential binding
domains. Also there are three so-call levels of structure in a protein, the
first is the sequence, the second is the local folding, and the third is the
overall shape of the protein. Usually you want to expose certain amino acid
sequences on the outside of the tertiary structure within specific
hydrophobic/hydrophilic regions. Also you have to be careful about the
protein structure you give it since it cannot have potential binding sites
that you don't want. Also often a couple of polypeptides will join together
to create a large/complex protein - sort of like the ribosome structure.
Also protein change shape sometimes when they bind with other cytoplasmic
entities.
Anyways, I might have some of it wrong but there is a lot of things that one
is trying to optimize in order to create a custom function protein.
Cheers,
-ben houston
http://www.exocortex.org/~ben
-----Original Message-----
From: owner-extropians@extropy.org [mailto:owner-extropians@extropy.org]On
Behalf Of Emlyn
Sent: Tuesday, February 13, 2001 1:51 AM
To: extropians@extropy.org
Subject: Re: Progress on the protein folding problem
Forgive my naivety... don't we want to go in the other direction? Specify a
shape, and have a computer tell us what sequence of amino acids we'd need to
use to achieve that?
Emlyn
----- Original Message -----
From: "Jeff Davis" <jdavis@socketscience.com>
To: <extropians@extropy.org>
Sent: Tuesday, February 13, 2001 1:12 PM
Subject: Progress on the protein folding problem
> Friends,
>
> I found the following on EurekAlert at:
>
> http://www.eurekalert.org/releases/hhmi-rmh021201.html
>
> >Rosetta may hold key to predicting protein folding
> >
> > February 12, 2001-A computational method developed by Howard Hughes
> Medical Institute investigator
> > David A. Baker and his colleagues has proven quite successful in
> predicting the three-dimensional structure of a
> > folded protein from its linear sequence of amino acids.
>
> The article does not say what computational resources were applied to the
> problem, but suffice it to say that it was not achieved with IBM's Blue
Gene.
>
> Perhaps the task is not so daunting as previously assumed.
>
>
> Best, Jeff Davis
>
> "Everything's hard till you know how to do it."
> Ray Charles
>
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